Metaheuristics based de novo protein sequencing: A new approach

被引：1

作者：

Boisson, Jean-Charles ^{[1
]}

Jourdan, Laetitia ^{[1
]}

Talbi, El-Ghazali ^{[1
]}

机构：

[1] INRIA Lille Nord Europe, F-59650 Villeneuve Dascq, France

来源：

APPLIED SOFT COMPUTING | 2011年 / 11卷 / 02期

关键词：

Cooperative metaheuristic; Protein identification; Genetic algorithm; Local search; IDENTIFICATION; OPTIMIZATION;

D O I：

10.1016/j.asoc.2010.08.007

中图分类号：

TP18 [人工智能理论];

学科分类号：

081104 ; 0812 ; 0835 ; 1405 ;

摘要：

In this article, a new approach is proposed for the de novo protein sequencing problem. The aim is to find the sequence of an experimental protein from only experimental data, i.e. without databases. To do so, a three-step model called SSO for Shape, Sequence and Order has been designed. No prior knowledge in genomics nor protein databases are used. Here we modelized de novo protein sequencing as a combinatorial optimisation problem and propose cooperative metaheuristics to solve it. Results are assessed on experimental proteins and proved the feasibility of this approach. (C) 2010 Elsevier B.V. All rights reserved.

引用

页码：2271 / 2278

页数：8

共 25 条

[1]

[Anonymous], 1975, Ann Arbor

[2]

[Anonymous], 2009, METAHEURISTICS DESIG, DOI DOI 10.1002/9780470496916

[3]

BOISSON JC, 2007, P 55 ASMS C MASS SPE, P3

[4] ParadisEO: A framework for the reusable design of parallel and distributed metaheuristics [J].

Cahon, S ;

Melab, N ;

Talbi, EG .

JOURNAL OF HEURISTICS, 2004, 10 (03) :357-380

[5] A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry [J].

Chen, T ;

Kao, MY ;

Tepel, M ;

Rush, J ;

Church, GM .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2001, 8 (03) :325-337

[6] De novo peptide sequencing via tandem mass spectrometry [J].

Dancík, V ;

Addona, TA ;

Clauser, KR ;

Vath, JE ;

Pevzner, PA .

JOURNAL OF COMPUTATIONAL BIOLOGY, 1999, 6 (3-4) :327-342

[7]

DAVIS L, 1989, PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON GENETIC ALGORITHMS, P61

[8] PepNovo: De novo peptide sequencing via probabilistic network modeling [J].

Frank, A ;

Pevzner, P .

ANALYTICAL CHEMISTRY, 2005, 77 (04) :964-973

[9]

Glover F., 1989, ORSA Journal on Computing, V1, P190, DOI [10.1287/ijoc.2.1.4, 10.1287/ijoc.1.3.190]

[10] Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data [J].

Heredia-Langner, A ;

Cannon, WR ;

Jarman, KD ;

Jarman, KH .

BIOINFORMATICS, 2004, 20 (14) :2296-2304

← 1 2 3 →